Running PDBSTAT from Linux Ayuda is on: /farm/software/PdbStat/PdbStat-5.7 (C) (C) Pdbstat -- A program to evaluate some statistics of macromolecules, (C) given the cartesian coordinates. (C) (C) (c) Copyright 1992-2012 Roberto Tejero and Gaetano T. Montelione (C) Center for Advanced Technology and Medicine (CABM) (C) Rutgers University (C) ** VERSION: 5.7-exp dom mar 10 23:17:04 UTC 2013 ** ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ===============> W E L C O M E to PDBStat <================ PDBStat has become a tool able (between other things) of: a) read and interconvert between DISMAN, DYANA, PDB, DISCOVER, IMPACT b) elaborate some info about the molecule as MW, Radius of gyration, .. c) investigate the setereochemical quality of a protein by evaluating phi, psi, chi1, impropers and chirality The sequence of acts should be: 1.- read a file (coords, constr) 2.- read a sequence file (can be free format) 3.- Follow menu (calculating, writing ...) NOTE: Be aware that if you read in a constraint file you *ALWAYS* need to read a sequence file also HAVE FUN AND ENJOY !! **** For more info type `help' or `menu' **** --> ... Reading/Loading Distances file ... 125 distance records read --> ... Reading/Loading Dihedral Library .. 1119 library records read PdbStat> [rea]d [hel]p [his]tory [men]u [phi] [qui]t... PdbStat> leyendo PDB > locate_file(): file `HR4435B_R3Cons_em_bcr3.pdb' opened for reading > ReadCoordsPdb(): >> EXPDTA NMR, 21 STRUCTURES > ReadCoordsPdb(): >> REMARK PdbStat -- ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ > ReadCoordsPdb(): >> REMARK PdbStat -- PDB COORDINATES FOR TEMP_BCM_111.PDB, 20 MODEL/S TEMP_BCM_111.PDB > ReadCoordsPdb(): >> REMARK PdbStat -- ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ > ReadCoordsPdb(): >> SEQRES 1 A 83 MET GLY HIS HIS HIS HIS HIS HIS SER HIS MET LEU PRO 1 > ReadCoordsPdb(): Counting models in file `HR4435B_R3Cons_em_bcr3.pdb'; Model: 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 > ReadCoordsPdb(): After scanning there is(are) 20 model(s) > ReadCoordsPdb(): what model do you want [(1 to 20) or all] ?_ > ReadCoordsPdb(): Reading *all* models in file HR4435B_R3Cons_em_bcr3.pdb > ReadCoordsPdb(): Reading a total of (20) models in file > ReadCoordsPdb(): I'm reading!, model 0 > ReadCoordsPdb(): *** SUMMARY *** > ReadCoordsPdb(): --> 26640 ATOM records read from file > ReadCoordsPdb(): --> 26640 Regular IUPAC Atoms > ReadCoordsPdb(): --> 0 Pseudo-atoms (DISMAN type) > ReadCoordsPdb(): --> 0 Lone pairs > ReadCoordsPdb(): Bye ... > ReadCoordsPdb(): ** monomer, 1 [1] chains ** PdbStat> > calc_order_parameters(): ... Evaluating Dihedrals CHAIN .GT. SUM.GT. RES ID DIH S(phi) S(psi) S(chi1) S(chi2) S(chi3) S(chi4) S(chi5) 0.90 1.6 ----------------------------------------------------------------------------------- MET A 1 0.579 0.733 0.430 0.290 GLY A 2 0.297 0.297 HIS A 3 0.583 0.330 0.558 0.719 HIS A 4 0.614 0.574 0.571 0.394 HIS A 5 0.752 0.318 0.598 0.578 HIS A 6 0.350 0.533 0.723 0.729 HIS A 7 0.683 0.424 0.486 0.367 HIS A 8 0.554 0.600 0.362 0.450 SER A 9 0.562 0.511 0.251 HIS A 10 0.574 0.726 0.928 0.724 MET A 11 0.994 0.968 0.869 0.439 0.139 11 11 LEU A 12 0.986 0.997 0.666 0.699 12 12 PRO A 13 0.991 0.966 0.960 0.936 13 13 PRO A 14 0.986 0.688 0.889 0.814 GLU A 15 0.652 0.590 0.656 0.307 0.827 GLN A 16 0.506 0.657 0.536 0.211 0.712 TRP A 17 0.776 0.860 0.996 0.901 SER A 18 0.883 0.987 0.662 18 HIS A 19 0.992 0.986 0.245 0.041 19 19 THR A 20 0.985 0.992 0.603 20 20 THR A 21 0.997 0.998 0.922 21 21 VAL A 22 0.999 0.997 0.856 22 22 ARG A 23 0.995 0.997 0.872 0.866 0.363 0.758 1.000 23 23 ASN A 24 0.998 0.998 1.000 0.999 24 24 ALA A 25 0.999 0.996 25 25 LEU A 26 0.999 0.995 0.786 0.867 26 26 LYS A 27 0.999 0.993 0.810 0.999 0.999 0.998 27 27 ASP A 28 0.988 0.999 0.998 0.960 28 28 LEU A 29 0.997 0.991 0.999 1.000 29 29 LEU A 30 0.987 0.975 0.813 0.782 30 30 LYS A 31 0.995 0.994 0.633 0.999 0.999 0.996 31 31 ASP A 32 0.989 0.970 0.922 0.971 32 32 MET A 33 0.978 0.979 0.716 0.745 0.259 33 33 ASN A 34 0.988 0.976 0.350 0.859 34 34 GLN A 35 0.995 0.996 0.681 0.957 0.660 35 35 SER A 36 0.996 0.996 0.419 36 36 SER A 37 0.997 0.996 0.708 37 37 LEU A 38 0.999 0.997 0.764 0.750 38 38 ALA A 39 0.999 0.998 39 39 LYS A 40 0.994 0.996 0.670 0.999 1.000 1.000 40 40 GLU A 41 0.993 0.993 0.997 0.652 0.923 41 41 CYS A 42 0.992 0.985 0.422 42 42 PRO A 43 0.991 0.888 0.913 0.831 43 LEU A 44 0.950 0.994 0.983 0.694 44 44 SER A 45 0.994 0.970 0.682 45 45 GLN A 46 0.998 0.997 0.999 0.997 0.955 46 46 SER A 47 0.998 0.997 0.681 47 47 MET A 48 0.996 0.997 0.723 0.405 0.119 48 48 ILE A 49 0.998 0.998 1.000 0.921 49 49 SER A 50 0.995 0.994 0.398 50 50 SER A 51 0.996 0.997 0.690 51 51 ILE A 52 0.992 0.991 0.918 0.921 52 52 VAL A 53 0.993 0.988 0.944 53 53 ASN A 54 0.982 0.946 0.999 0.981 54 54 SER A 55 0.284 0.603 0.557 THR A 56 0.842 0.891 0.514 56 TYR A 57 0.971 0.792 0.850 0.992 TYR A 58 0.778 0.427 0.374 0.977 ALA A 59 0.465 0.311 ASN A 60 0.513 0.621 0.414 0.883 VAL A 61 0.861 0.953 0.273 61 SER A 62 0.990 0.959 0.668 62 62 ALA A 63 0.997 0.998 63 63 ALA A 64 0.999 0.997 64 64 LYS A 65 0.995 0.998 0.997 0.310 0.988 0.997 65 65 CYS A 66 0.990 0.996 0.815 66 66 GLN A 67 0.998 0.996 0.622 0.519 0.813 67 67 GLU A 68 0.998 0.992 0.934 0.618 0.914 68 68 PHE A 69 0.998 0.997 0.996 0.994 69 69 GLY A 70 0.999 0.998 70 70 ARG A 71 0.999 0.997 0.649 0.998 0.534 0.633 1.000 71 71 TRP A 72 0.998 0.998 0.998 0.999 72 72 TYR A 73 0.998 0.997 0.993 0.996 73 73 LYS A 74 0.997 0.994 0.802 0.947 0.794 0.999 74 74 HIS A 75 0.982 0.991 0.999 0.127 75 75 PHE A 76 0.998 0.996 0.999 0.998 76 76 LYS A 77 0.972 0.963 0.562 0.549 0.923 0.674 77 77 LYS A 78 0.383 0.556 0.683 0.999 0.999 0.999 THR A 79 0.442 0.542 0.436 LYS A 80 0.285 0.584 0.479 0.791 0.999 0.999 ASP A 81 0.718 0.353 0.539 0.944 MET A 82 0.575 0.253 0.627 0.426 0.427 MET A 83 0.568 0.515 0.294 0.494 Ranges: 4 from: A 11 to A 13 from: A 19 to A 42 from: A 44 to A 54 from: A 62 to A 77 PdbStat> > do_average_coords(): Making average for backbone atoms > do_average_coords(): Calculating center of masses > do_average_coords(): Calling optimal rotation for backbone onto model 1 > do_average_coords(): Calc. average coordinates backbone > Kabsch RMSD of backbone atoms in res. A[11..13],A[19..42],A[44..54],A[62..77],for model 1 is: 0.917 > Kabsch RMSD of backbone atoms in res. A[11..13],A[19..42],A[44..54],A[62..77],for model 2 is: 0.599 (*) > Kabsch RMSD of backbone atoms in res. A[11..13],A[19..42],A[44..54],A[62..77],for model 3 is: 0.994 > Kabsch RMSD of backbone atoms in res. A[11..13],A[19..42],A[44..54],A[62..77],for model 4 is: 0.797 > Kabsch RMSD of backbone atoms in res. A[11..13],A[19..42],A[44..54],A[62..77],for model 5 is: 0.702 > Kabsch RMSD of backbone atoms in res. A[11..13],A[19..42],A[44..54],A[62..77],for model 6 is: 0.990 > Kabsch RMSD of backbone atoms in res. A[11..13],A[19..42],A[44..54],A[62..77],for model 7 is: 0.889 > Kabsch RMSD of backbone atoms in res. A[11..13],A[19..42],A[44..54],A[62..77],for model 8 is: 0.951 > Kabsch RMSD of backbone atoms in res. A[11..13],A[19..42],A[44..54],A[62..77],for model 9 is: 1.201 > Kabsch RMSD of backbone atoms in res. A[11..13],A[19..42],A[44..54],A[62..77],for model 10 is: 0.621 > Kabsch RMSD of backbone atoms in res. A[11..13],A[19..42],A[44..54],A[62..77],for model 11 is: 0.673 > Kabsch RMSD of backbone atoms in res. A[11..13],A[19..42],A[44..54],A[62..77],for model 12 is: 1.358 > Kabsch RMSD of backbone atoms in res. A[11..13],A[19..42],A[44..54],A[62..77],for model 13 is: 0.662 > Kabsch RMSD of backbone atoms in res. A[11..13],A[19..42],A[44..54],A[62..77],for model 14 is: 1.054 > Kabsch RMSD of backbone atoms in res. A[11..13],A[19..42],A[44..54],A[62..77],for model 15 is: 1.219 > Kabsch RMSD of backbone atoms in res. A[11..13],A[19..42],A[44..54],A[62..77],for model 16 is: 1.100 > Kabsch RMSD of backbone atoms in res. A[11..13],A[19..42],A[44..54],A[62..77],for model 17 is: 0.943 > Kabsch RMSD of backbone atoms in res. A[11..13],A[19..42],A[44..54],A[62..77],for model 18 is: 0.742 > Kabsch RMSD of backbone atoms in res. A[11..13],A[19..42],A[44..54],A[62..77],for model 19 is: 0.676 > Kabsch RMSD of backbone atoms in res. A[11..13],A[19..42],A[44..54],A[62..77],for model 20 is: 0.946 > > Kabsch RMSD statistics for 20 structures: > Mean RMSD using as refer. str. `average' for res.[11..13],[19..42],[44..54],[62..77], is: 0.902 > Range of RMSD values to reference struct. is 0.599 to 1.358 > do_average_coords(): Making average for heavy atoms > do_average_coords(): Calculating center of masses > do_average_coords(): Calling optimal rotation for heavy onto model 1 > do_average_coords(): Calc. average coordinates heavy > Kabsch RMSD of heavy atoms in res. A[11..13],A[19..42],A[44..54],A[62..77],for model 1 is: 1.222 > Kabsch RMSD of heavy atoms in res. A[11..13],A[19..42],A[44..54],A[62..77],for model 2 is: 1.011 (*) > Kabsch RMSD of heavy atoms in res. A[11..13],A[19..42],A[44..54],A[62..77],for model 3 is: 1.265 > Kabsch RMSD of heavy atoms in res. A[11..13],A[19..42],A[44..54],A[62..77],for model 4 is: 1.124 > Kabsch RMSD of heavy atoms in res. A[11..13],A[19..42],A[44..54],A[62..77],for model 5 is: 1.103 > Kabsch RMSD of heavy atoms in res. A[11..13],A[19..42],A[44..54],A[62..77],for model 6 is: 1.514 > Kabsch RMSD of heavy atoms in res. A[11..13],A[19..42],A[44..54],A[62..77],for model 7 is: 1.213 > Kabsch RMSD of heavy atoms in res. A[11..13],A[19..42],A[44..54],A[62..77],for model 8 is: 1.250 > Kabsch RMSD of heavy atoms in res. A[11..13],A[19..42],A[44..54],A[62..77],for model 9 is: 1.447 > Kabsch RMSD of heavy atoms in res. A[11..13],A[19..42],A[44..54],A[62..77],for model 10 is: 1.114 > Kabsch RMSD of heavy atoms in res. A[11..13],A[19..42],A[44..54],A[62..77],for model 11 is: 1.209 > Kabsch RMSD of heavy atoms in res. A[11..13],A[19..42],A[44..54],A[62..77],for model 12 is: 1.836 > Kabsch RMSD of heavy atoms in res. A[11..13],A[19..42],A[44..54],A[62..77],for model 13 is: 1.073 > Kabsch RMSD of heavy atoms in res. A[11..13],A[19..42],A[44..54],A[62..77],for model 14 is: 1.446 > Kabsch RMSD of heavy atoms in res. A[11..13],A[19..42],A[44..54],A[62..77],for model 15 is: 1.592 > Kabsch RMSD of heavy atoms in res. A[11..13],A[19..42],A[44..54],A[62..77],for model 16 is: 1.530 > Kabsch RMSD of heavy atoms in res. A[11..13],A[19..42],A[44..54],A[62..77],for model 17 is: 1.270 > Kabsch RMSD of heavy atoms in res. A[11..13],A[19..42],A[44..54],A[62..77],for model 18 is: 1.312 > Kabsch RMSD of heavy atoms in res. A[11..13],A[19..42],A[44..54],A[62..77],for model 19 is: 1.132 > Kabsch RMSD of heavy atoms in res. A[11..13],A[19..42],A[44..54],A[62..77],for model 20 is: 1.374 > > Kabsch RMSD statistics for 20 structures: > Mean RMSD using as refer. str. `average' for res.[11..13],[19..42],[44..54],[62..77], is: 1.302 > Range of RMSD values to reference struct. is 1.011 to 1.836 PdbStat> PdbStat> *END* of program detected, BYE! ...